I had a similar problem in Linux mint with LXDE, every time i started or rebooted my system the mouse pointer resets to the default even when i edited the Xorg.conf file with mouse acceleration options, it simply didn't work.
What worked for me was editing the file /home/yourusername/.config/lxsession/LXDE/desktop.conf
I edited the [mouse] section of the file like this:
[Mouse]
AccFactor=70
AccThreshold=1
LeftHanded=0
then i rebooted the system and it worked. Note that this is my personal setup wich is faster than the default.
My pointer had since then the velocity i want. I have to mention that AccFactor only worked with values of tens (10,20,70 etc) and the AccThreshold at 1.
I think every desktop enviroment has its own configuration file, and most of them have a gui to acces the configuration, but i don't know what happen with lxde that doesn't save the changes of the mouse pointer or they are overidden every time the system starts.
Hope this could help you.
P.S. sorry if i have mistakes in my writting, i'm still learning english.